Get the mechanical part of it (removing front cover, adjusting chain etc.) out of your head. If the motor ran fine before it was removed you shouldn't have to touch any of that. You probably don't have to touch the ignition timing either if it ran fine. Install the motor, start it up and see how it runs now.
Take a look at the video Mark posted. It will go a long way in helping your understanding of the ignition system.
Take a look at the video Mark posted. It will go a long way in helping your understanding of the ignition system.
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